8FWD

Fast and versatile sequence- independent protein docking for nanomaterials design using RPXDock

8FWD の概要

• エントリーDOI: 10.2210/pdb8fwd/pdb
• EMDBエントリー: 29502
• 分子名称: O43-rpxdoc-EK1_A, O43-rpxdoc-EK1_B (2 entities in total)
• 機能のキーワード: octahedra, oligomer, de novo design, rosetta, cryoem, interface, de novo protein
• 由来する生物種: synthetic construct; 詳細
• タンパク質・核酸の鎖数: 48
• 化学式量合計: 1005427.78

構造登録者

Skotheim, R.,Borst, A.J.,Baker, D. (登録日: 2023-01-20, 公開日: 2023-05-10, 最終更新日: 2025-06-04)

主引用文献

Sheffler, W.,Yang, E.C.,Dowling, Q.,Hsia, Y.,Fries, C.N.,Stanislaw, J.,Langowski, M.D.,Brandys, M.,Li, Z.,Skotheim, R.,Borst, A.J.,Khmelinskaia, A.,King, N.P.,Baker, D.
Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock.
Plos Comput.Biol., 19:e1010680-e1010680, 2023

PubMed Abstract: Computationally designed multi-subunit assemblies have shown considerable promise for a variety of applications, including a new generation of potent vaccines. One of the major routes to such materials is rigid body sequence-independent docking of cyclic oligomers into architectures with point group or lattice symmetries. Current methods for docking and designing such assemblies are tailored to specific classes of symmetry and are difficult to modify for novel applications. Here we describe RPXDock, a fast, flexible, and modular software package for sequence-independent rigid-body protein docking across a wide range of symmetric architectures that is easily customizable for further development. RPXDock uses an efficient hierarchical search and a residue-pair transform (RPX) scoring method to rapidly search through multidimensional docking space. We describe the structure of the software, provide practical guidelines for its use, and describe the available functionalities including a variety of score functions and filtering tools that can be used to guide and refine docking results towards desired configurations.

PubMed: 37216343
DOI: 10.1371/journal.pcbi.1010680

実験手法

ELECTRON MICROSCOPY (3.67 Å)